src/hg/makeDb/trackDb/tRNAs.html 1.2

Index: src/hg/makeDb/trackDb/tRNAs.html
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/tRNAs.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -b -B -U 4 -r1.1 -r1.2
--- src/hg/makeDb/trackDb/tRNAs.html	15 Jan 2010 15:37:58 -0000	1.1
+++ src/hg/makeDb/trackDb/tRNAs.html	23 Jan 2010 00:15:29 -0000	1.2
@@ -15,8 +15,21 @@
 Detailed tRNA annotations for eukaryotes, bacteria, and archaea are available at
 <A HREF="http://gtrnadb.ucsc.edu" TARGET=_blank>Genomic tRNA Database (GtRNAdb)</A>. 
 </P>
 <P>
+What does the tRNAscan-SE score mean?  Anything with a score above 20 bits is likely to be
+<I>derived</I> from a tRNA, although this does not indicate whether the tRNA gene still encodes a 
+functional tRNA molecule (i.e. tRNA-derived SINES probably do not function in the ribosome in translation).
+For vertebrate tRNAs, we believe a score of >60.0 (bits) are likely to encode functional tRNA genes, and 
+those with scores below ~45 have sequence or structural features that indicate they probably are
+no longer involved in translation.  tRNAs with scores between 45-60 bits are in the "grey" zone, and may
+or may not have all the required features to be functional.  In these cases, tRNAs should be inspected
+carefully for loss of specific primary or secondary structure features (usually in alignments with other
+genes of the same isotype), in order to make a better educated guess.  These rough score range guides 
+are not exact, nor are they based on specific biochemical studies of atypical tRNA features,
+so please treat them accordingly.
+</P>
+<P>
 Both tRNAscan-SE and GtRNAdb are maintained by the 
 <A HREF="http://lowelab.ucsc.edu" TARGET=_blank>Lowe Lab</A> at UCSC.
 </P>